loci.formats.services

Class WlzServiceImpl

java.lang.Object

loci.common.services.AbstractService

loci.formats.services.WlzServiceImpl

All Implemented Interfaces:

Service, WlzService

public class WlzServiceImpl
extends AbstractService
implements WlzService

Field Summary

Fields

Modifier and Type	Field and Description
private uk.ac.mrc.hgu.Wlz.WlzIBox3	bBox
static String	NO_WLZ_MSG
private int	objGType
private int	objType
private int	pixelType
private int	state
private uk.ac.mrc.hgu.Wlz.WlzDVertex3	voxSz
static String	WLZ_ORG_LABEL
static int	WLZ_SERVICE_READ
static int	WLZ_SERVICE_UNKNOWN
static int	WLZ_SERVICE_WRITE
private uk.ac.mrc.hgu.Wlz.WlzFileStream	wlzFP
private uk.ac.mrc.hgu.Wlz.WlzObject	wlzObj
private String	wlzVersion

Constructor Summary

Constructors

Constructor and Description
WlzServiceImpl()

Method Summary

Methods

Modifier and Type	Method and Description
protected void	checkClassDependency(Class<? extends Object> klass) Checks a given class dependency at runtime to ensure that a given class will be available.
void	close() Closes the file.
String	getNoWlzMsg() Gets the text string for when Woolz has not been found.
double	getOrgX() Gets column origin.
double	getOrgY() Gets line origin.
double	getOrgZ() Gets plane origin.
int	getPixelType() Gets the image pixel type.
int	getSizeC() Gets number of channels.
int	getSizeT() Gets number of time samples.
int	getSizeX() Gets width in pixels/voxels.
int	getSizeY() Gets height in pixels/voxels.
int	getSizeZ() Gets depth (number of x-y planes) in voxels.
int[]	getSupPixelTypes() Gets supported pixel types.
double	getVoxSzX() Gets voxel width.
double	getVoxSzY() Gets voxel height.
double	getVoxSzZ() Gets voxel depth.
String	getWlzOrgLabelName() Gets the text string used for the Woolz origin label.
boolean	isRGB() Gets boolean for whether image is colour or not.
void	open(String file, String rw) Initializes the service for the given file path.
private void	openRead(String file)
private void	openWrite(String file)
byte[]	readBytes(int no, byte[] buf, int x, int y, int w, int h) Reads a rectangle of bytes in an x-y plane from the opened Woolz object.
private byte[]	readBytes2DDomObj(byte[] buf, int x, int y, int w, int h)
private byte[]	readBytes3DDomObj(byte[] buf, int x, int y, int z, int w, int h)
void	saveBytes(int no, byte[] buf, int x, int y, int w, int h) Adds a rectangle of bytes in an x-y plane to the opened Woolz object.
void	setupWrite(int orgX, int orgY, int orgZ, int pixSzX, int pixSzY, int pixSzZ, int pixSzC, int pixSzT, double voxSzX, double voxSzY, double voxSzZ, int gType) Sets up the service, which must have already been opened for writing.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

WLZ_ORG_LABEL

public static final String WLZ_ORG_LABEL

See Also:

Constant Field Values

NO_WLZ_MSG

public static final String NO_WLZ_MSG

See Also:

Constant Field Values

WLZ_SERVICE_UNKNOWN

public static final int WLZ_SERVICE_UNKNOWN

See Also:

Constant Field Values

WLZ_SERVICE_READ

public static final int WLZ_SERVICE_READ

See Also:

Constant Field Values

WLZ_SERVICE_WRITE

public static final int WLZ_SERVICE_WRITE

See Also:

Constant Field Values

state

private int state

pixelType

private int pixelType

objType

private int objType

objGType

private int objGType

wlzVersion

private String wlzVersion

bBox

private uk.ac.mrc.hgu.Wlz.WlzIBox3 bBox

voxSz

private uk.ac.mrc.hgu.Wlz.WlzDVertex3 voxSz

wlzObj

private uk.ac.mrc.hgu.Wlz.WlzObject wlzObj

wlzFP

private uk.ac.mrc.hgu.Wlz.WlzFileStream wlzFP

Constructor Detail

WlzServiceImpl

public WlzServiceImpl()

Method Detail

checkClassDependency

protected void checkClassDependency(Class<? extends Object> klass)

Description copied from class: AbstractService

Checks a given class dependency at runtime to ensure that a given class will be available. This method is expected to be called at least once by all service implementations.

Overrides:

checkClassDependency in class AbstractService

Parameters:

klass - A class that this service depends upon.

getNoWlzMsg

public String getNoWlzMsg()

Description copied from interface: WlzService

Gets the text string for when Woolz has not been found.

Specified by:

getNoWlzMsg in interface WlzService

getWlzOrgLabelName

public String getWlzOrgLabelName()

Description copied from interface: WlzService

Gets the text string used for the Woolz origin label.

Specified by:

getWlzOrgLabelName in interface WlzService

open

public void open(String file,
        String rw)
          throws FormatException,
                 IOException

Description copied from interface: WlzService

Initializes the service for the given file path.

Specified by:

open in interface WlzService

Parameters:

file - File path with which to initialize the service.

Throws:

FormatException

IOException

getSizeX

public int getSizeX()

Description copied from interface: WlzService

Gets width in pixels/voxels.

Specified by:

getSizeX in interface WlzService

Returns:

width.

getSizeY

public int getSizeY()

Description copied from interface: WlzService

Gets height in pixels/voxels.

Specified by:

getSizeY in interface WlzService

Returns:

height.

getSizeZ

public int getSizeZ()

Description copied from interface: WlzService

Gets depth (number of x-y planes) in voxels.

Specified by:

getSizeZ in interface WlzService

Returns:

depth.

getSizeC

public int getSizeC()

Description copied from interface: WlzService

Gets number of channels.

Specified by:

getSizeC in interface WlzService

Returns:

channels.

getSizeT

public int getSizeT()

Description copied from interface: WlzService

Gets number of time samples.

Specified by:

getSizeT in interface WlzService

Returns:

time.

isRGB

public boolean isRGB()

Description copied from interface: WlzService

Gets boolean for whether image is colour or not.

Specified by:

isRGB in interface WlzService

Returns:

true if image is colour.

getVoxSzX

public double getVoxSzX()

Description copied from interface: WlzService

Gets voxel width.

Specified by:

getVoxSzX in interface WlzService

Returns:

voxel width.

getVoxSzY

public double getVoxSzY()

Description copied from interface: WlzService

Gets voxel height.

Specified by:

getVoxSzY in interface WlzService

Returns:

voxel height.

getVoxSzZ

public double getVoxSzZ()

Description copied from interface: WlzService

Gets voxel depth.

Specified by:

getVoxSzZ in interface WlzService

Returns:

voxel depth.

getOrgX

public double getOrgX()

Description copied from interface: WlzService

Gets column origin.

Specified by:

getOrgX in interface WlzService

Returns:

column origin.

getOrgY

public double getOrgY()

Description copied from interface: WlzService

Gets line origin.

Specified by:

getOrgY in interface WlzService

Returns:

line origin.

getOrgZ

public double getOrgZ()

Description copied from interface: WlzService

Gets plane origin.

Specified by:

getOrgZ in interface WlzService

Returns:

plane origin.

getSupPixelTypes

public int[] getSupPixelTypes()

Description copied from interface: WlzService

Gets supported pixel types.

Specified by:

getSupPixelTypes in interface WlzService

Returns:

array of supported pixel types.

getPixelType

public int getPixelType()

Description copied from interface: WlzService

Gets the image pixel type.

Specified by:

getPixelType in interface WlzService

Returns:

pixel type.

setupWrite

public void setupWrite(int orgX,
              int orgY,
              int orgZ,
              int pixSzX,
              int pixSzY,
              int pixSzZ,
              int pixSzC,
              int pixSzT,
              double voxSzX,
              double voxSzY,
              double voxSzZ,
              int gType)
                throws FormatException

Description copied from interface: WlzService

Sets up the service, which must have already been opened for writing.

Specified by:

setupWrite in interface WlzService

Parameters:

orgX - x origin.

orgY - y origin.

orgZ - z origin (set to 0 for 2D).

pixSzX - width.

pixSzY - height.

pixSzZ - depth (number of planes, set to 1 for 2D).

pixSzC - number of channels.

pixSzT - number of time samples.

voxSzX - pixel/voxel width.

voxSzY - pixel/voxel heigth.

voxSzZ - voxel deoth.

gType - image value type.

Throws:

FormatException

close

public void close()
           throws IOException

Description copied from interface: WlzService

Closes the file.

Specified by:

close in interface WlzService

Throws:

IOException

readBytes

public byte[] readBytes(int no,
               byte[] buf,
               int x,
               int y,
               int w,
               int h)
                 throws FormatException,
                        IOException

Description copied from interface: WlzService

Reads a rectangle of bytes in an x-y plane from the opened Woolz object.

Specified by:

readBytes in interface WlzService

Parameters:

no - plane coordinate (set to 0 for 2D).

buf - buffer for bytes.

x - rectangle first column.

y - rectangle first line.

w - rectangle width (in columns).

h - rectangle heigth (in lines).

Returns:

Buffer of bytes read.

Throws:

FormatException

IOException

saveBytes

public void saveBytes(int no,
             byte[] buf,
             int x,
             int y,
             int w,
             int h)
               throws FormatException,
                      IOException

Description copied from interface: WlzService

Adds a rectangle of bytes in an x-y plane to the opened Woolz object.

Specified by:

saveBytes in interface WlzService

Parameters:

no - plane coordinate (set to 0 for 2D).

buf - buffer with bytes.

x - rectangle first column.

y - rectangle first line.

w - rectangle width (in columns).

h - rectangle heigth (in lines).

Throws:

FormatException

IOException

openRead

private void openRead(String file)
               throws FormatException,
                      IOException

Throws:

FormatException

IOException

openWrite

private void openWrite(String file)
                throws FormatException,
                       IOException

Throws:

FormatException

IOException

readBytes2DDomObj

private byte[] readBytes2DDomObj(byte[] buf,
                       int x,
                       int y,
                       int w,
                       int h)
                          throws uk.ac.mrc.hgu.Wlz.WlzException

Throws:

uk.ac.mrc.hgu.Wlz.WlzException

readBytes3DDomObj

private byte[] readBytes3DDomObj(byte[] buf,
                       int x,
                       int y,
                       int z,
                       int w,
                       int h)
                          throws uk.ac.mrc.hgu.Wlz.WlzException

Throws:

uk.ac.mrc.hgu.Wlz.WlzException